Add conda install kofamscan

[bryshalm]

In the dib-lab metagenomics rotation project

Annotating amino acid sequences

after

conda create -n kofamscan hmmer parallel ruby conda activate kofamscan

then installing kofamscan needs to be added (as explained by Tessa)

conda install kofamscan

Then checked with . . . . though not necessarily

exec_annotation -h

also if you could explain that kofamscan looks for a config file without have to call for it in the exec_annotation command would be helpful for newbies like me

[bluegenes]

I think after this, we figured out that we do actually need to explicitly pass in the config file.

So the commands should now read:

exec_annotation -f mapper --config config.yml -o query_nbhd_plass.clean_kofamscan.txt query_nbhd_plass.cdhit.fa 

and

exec_annotation -f mapper --config config.yml -o GCA_001508995.1_ASM150899v1_protein_kofamscan.txt GCA_001508995.1_ASM150899v1_protein.faa